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Search: Posts Made By: SamCurt
Forum: Bioinformatics 06-28-2017, 12:13 PM
Replies: 3
Views: 796
Posted By SamCurt
In that case, you used the wrong program. Before...

In that case, you used the wrong program. Before bcftools 1.0 the output of mpileup is called with bcftools view, but after that version the correct program should be bcftools call. So the command...
Forum: Bioinformatics 06-28-2017, 12:01 PM
Replies: 1
Views: 2,154
Posted By SamCurt
Please check the Bioconductor package tximport,...

Please check the Bioconductor package tximport, which reverse-calculate read counts from FPKM/TPM, with two modes.
Forum: Bioinformatics 06-28-2017, 11:56 AM
Replies: 218
Views: 134,454
Posted By SamCurt
Hi Alex, I understand that with --quantMode...

Hi Alex,
I understand that with --quantMode TranscriptomeSAM --quantTranscriptomeBan Singleend I can generate a transcript-coordinate bam file with indels and soft-clips. But do you consider it...
Forum: Bioinformatics 06-28-2017, 11:51 AM
Replies: 3
Views: 796
Posted By SamCurt
Hi, Which version of bcftools are you using?...

Hi,

Which version of bcftools are you using? bcftools view are two different programs before and after 1.0. My guess is the -b argument in bcftools that's the problem, since it makes a BCF output....
Forum: Bioinformatics 03-20-2017, 11:37 AM
Replies: 2
Views: 1,065
Posted By SamCurt
Of course I know things like DESeq2 can't take...

Of course I know things like DESeq2 can't take TPM. The options I mentioned above are:

Take the TPM from the quantifier directly to downstream.
Take the expected read count from the quantifier,...
Forum: Bioinformatics 03-20-2017, 11:24 AM
Replies: 2
Views: 1,065
Posted By SamCurt
The necessarity of between-sample normalization?

I'm currently perform some analyses involving cross-project expression data. Because it involves linear equations, we have decided to take log(TPM) as that algorithm's input.

While using older...
Forum: Bioinformatics 01-04-2017, 03:28 AM
Replies: 5
Views: 1,568
Posted By SamCurt
The complete code for one of those sets--the one...

The complete code for one of those sets--the one I mentioned to currently only have "open" counts data" is available open source (I already saw the code). I just want to know how many days would I...
Forum: Bioinformatics 01-03-2017, 12:33 PM
Replies: 5
Views: 1,568
Posted By SamCurt
The biggest problem is some of the data used has...

The biggest problem is some of the data used has non-public SAM/BAMs, so I have to live with count-level data. This is not to mention some of these sets use Ensembl IDs, some use EntrezGene IDs and...
Forum: Bioinformatics 01-02-2017, 01:12 PM
Replies: 5
Views: 1,568
Posted By SamCurt
Rebasing gene lengths when combining the FPKMs of several studies

We're planning to combine FPKMs of several GEO datasets for our project. However, these projects uses different gene annotations on GRCh37--some use hg37 and some use hg19--for their gene counting.
...
Forum: Bioinformatics 11-03-2016, 11:23 AM
Replies: 0
Views: 747
Posted By SamCurt
Transforming Read Counts for Linear Regression--which to use?

I've to transform some RNA-seq read counts into linear regressions algorithms that were originally written for microarray data.

Not that I don't know how to transform read counts for linear...
Forum: Bioinformatics 09-20-2016, 10:49 AM
Replies: 1
Views: 2,790
Posted By SamCurt
No, that's the genomic sequence. For these you'd...

No, that's the genomic sequence. For these you'd need to check the major genome databases; I guess you mean these:

NCBI: ftp://ftp.ncbi.nih.gov/refseq/D_rerio/mRNA_Prot/zebrafish.1.rna.fna.gz
...
Forum: RNA Sequencing 09-09-2016, 03:22 PM
Replies: 4
Views: 1,758
Posted By SamCurt
Well, as I mentioned I'd still need to do STAR...

Well, as I mentioned I'd still need to do STAR alignments for variant calling, so if it gives a sufficiently accurate gene count, probably I'd go for it.

But as transcript-level counting is...
Forum: RNA Sequencing 09-09-2016, 03:10 PM
Replies: 1
Views: 778
Posted By SamCurt
You're have to realign first to the same...

You're have to realign first to the same reference, or else it's an orange-apple case.
Forum: RNA Sequencing 09-09-2016, 10:44 AM
Replies: 4
Views: 1,758
Posted By SamCurt
Gene-level Quantification

Currently I still use htseq-count to perform gene-level quantification (and RSEM for transcript-level by the way), but I found htseq-count being overly cumbersome to use, requiring re-sorting...
Forum: RNA Sequencing 08-19-2016, 01:43 PM
Replies: 1
Views: 843
Posted By SamCurt
Alternate Contigs and Gene expression profiling

Currently I do my RNAseq analyses using the primary-assembly-only version of GRCh/GRCm38 from GENCODE, and their annotations thereof.

Upon reading Broad's recent guide on alt-contig-aware variant...
Forum: Bioinformatics 07-07-2016, 11:32 AM
Replies: 4
Views: 1,811
Posted By SamCurt
If you want a p-value, you may as well check...

If you want a p-value, you may as well check NOISeq on Bioconductor.
Forum: Bioinformatics 07-07-2016, 10:49 AM
Replies: 4
Views: 1,811
Posted By SamCurt
By "single replicate" you mean just one sample...

By "single replicate" you mean just one sample per condition, or two?
Forum: Bioinformatics 05-02-2016, 09:55 AM
Replies: 218
Views: 134,454
Posted By SamCurt
So, just for gene expression profiling purposes,...

So, just for gene expression profiling purposes, should I keep my sjDb file set for second-pass alignment constant?

Complete story: I have a set of ~40 samples already completed the entire set of...
Forum: Bioinformatics 04-25-2016, 08:51 AM
Replies: 3
Views: 1,343
Posted By SamCurt
I don't understand what you mean here. While you...

I don't understand what you mean here. While you understand "detecting differential expressed genes for two samples is not possible" without biological replicates, how do you "based on [fold change]...
Forum: Bioinformatics 04-05-2016, 09:42 PM
Replies: 218
Views: 134,454
Posted By SamCurt
Thank you for the quick reply, Alex. I also...

Thank you for the quick reply, Alex.

I also have another problem here. My new institution only has 2.4.0j on their cluster, and it'd take about a week to get a newer version installed. Do you...
Forum: Bioinformatics 04-04-2016, 10:08 AM
Replies: 218
Views: 134,454
Posted By SamCurt
Just a quick question here. Is the parameters...

Just a quick question here. Is the parameters file used with --parametersFile just a list of command-line options in the same way I type in the console?
Forum: Bioinformatics 12-03-2012, 01:32 PM
Replies: 0
Views: 1,153
Posted By SamCurt
Is FPKM a good substitute for microarray expression levels?

A few months ago I have asked here whether FPKMs in general can be used like microarray expression levels. While Dr Anders has kindly gave his opinion (that some transformation (such as log) might be...
Forum: Bioinformatics 09-12-2012, 07:59 AM
Replies: 2
Views: 1,103
Posted By SamCurt
Hi Simon, Not that I haven't did literature...

Hi Simon,

Not that I haven't did literature search before, but the answer is inconclusive. While I can generally conclude microarray methods can be applied to FPKMs (or in some cases raw counts),...
Forum: Bioinformatics 09-11-2012, 01:21 PM
Replies: 2
Views: 1,103
Posted By SamCurt
Performing eQTL on FPKMs?

We are planning to perform an eQTL analysis where the genotype input, at this time, will only be from a previous genotyping microarray run.

In this case, would it still be appropriate for us to...
Forum: Bioinformatics 12-29-2011, 02:08 PM
Replies: 0
Views: 796
Posted By SamCurt
Doing DEG for a suspected new transcript?

Hi all,

I have reviewed some of my mRNA-seq results and have noticed that both Scripture and Cufflinks' model reported a transcript located in my locus of interest and between two of our long-time...
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